Working Group: Imaging Flow Cytometry
Good water and air quality as well as pollination are of high relevance to our daily life and are linked to microscopic small organisms or particles (phytoplankton organisms and pollen). For high throughput air and water quality, as well as pollination assessment, a worldwide unique cytometer configuration allows to measure several thousands of microscopic images in short time of seconds to minutes. In combination with deep learning technologies we aim to develop a pioneering new technology of automated high throughput species recognition. The achievement of this ambitious vision is only possible with interdisciplinary work and the strong support by many cooperation partners.
Besides the establishment of automated species recognition, we already use imaging flow cytometry in trait-based physiological experiments to investigate coexistence and resilience mechanisms of phytoplankton organisms.
News
Video-portait about our work: Video
Press release 10/2021: UFZ
LVZ 09/2021: LVZ
Sächsiche Zeitung 02/2021: SZ
PlanktAI - Phytoplankton identification using AI - PIs: Dr. Jana Wäldchen, Dr. Ladislav Hrodac, Dr. Susanne Dunker
SedimentAI - Automated particle detection in Sediments using imaging flow-cytometry and Artificial Intelligence (SedimentAI). PIs: Dr. Susanne Dunker, Prof. Dr. Ulrike Herzschuh, Dr. Thomas Hornick, Dr. Kathleen Stoof-Leichsenring, Prof. Dr. Bogdan Franczyk, Prof. Dr. Patrick Mäder (funded by HelmholtzAI grant)
PhenObs - PhenObs is a global network of botanical gardens bringing together researchers, students and citizen scientists to learn more about the impacts of climate change on the phenology of herbaceous plant species (PhenObs).
HistColNet - Historical collections: a window into the impacts of decades of anthropogenic change on plant-pollinator interactions - PIs: Dr. Demetra Rakosy, Dr. Susanne Dunker, Dr. Thomas Hornick (funded by the iDiv Flexpool DFG grant)
iNutriPol - Assessing the impact of the nutritional value of pollen diversity for soil food webs - PI: Dr. Thomas Hornick, Co-PIs: Dr. Simone Cesarz, Dr. Susanne Dunker, PD Dr. Mika Tarkka, Prof. Dr. Severin Sasso, Dr. Ronny Richter (funded by the iDiv Flexpool DFG grant)
iNTERACT - impacts of laNdscape structure, floral resources and land-use intensity on the healTh of bEneficial aRthropods in AgroeCosysTems - PI: Dr. Christophe Dominik, Co-PIs: Dr. Oliver Schweiger, Dr. Tesfaye Wubet, Dr. Susanne Dunker, Prof. Dr. Robert Paxton, Prof. Dr. Severin Sasso, Dr. Panagiotis Theodorou (funded by the iDiv Flexpool DFG grant)
Nutribee - Interaktion von abiotischen Stressoren und Nahrungslimitierung auf Bienengesundheit und Entwicklung von Jungvölkern im Freiland - PI Dr. Silvio Erler, Projektpartner: Julius Kühn-Institut (JKI), Institut für Bienenkunde, Nds. Landesamt für Verbraucherschutz und Lebensmittelsicherheit, Institut für Bienenkunde und Imkerei (IBI), Ruhr-Universität Bochum, Freie Universität Berlin, Technische Universität Ilmenau, Universität Hohenheim (funded by the BMEL/BÖLN)
iCyt - integrative Cytomics (iCyt) support unit 
- PI: Prof. Dr. Stan Harpole, Co-PIs: Dr. Susanne Dunker, Prof. Dr. Severin Sasso, Dr. Torsten Jakob, Prof. Dr. Patrick Mäder, Dr. Jan Bumberger (funded by the iDiv Flexpool DFG grant)
PolDiv - Automated high throughput pollen diversity monitoring to study the ecosystem services air quality regulation and pollination (wind and insect pollination) - PIs: Dr. Susanne Dunker, Prof. Dr. Stan Harpole, Dr. Jan Bumberger, Prof. Dr. Peter Dietrich, Dr. Anett Richter, Prof. Dr. Aletta Bonn, Prof. Dr. Regina Treudler, Prof. Dr. Tiffany Knight, Dr. Jana Wäldchen, Prof. Dr. Patrick Mäder (funded by the iDiv Flexpool DFG grant) -
ResBioDiv - A mechanistic test of resilience provisioning of biodiversity across environmental gradients - PIs: Prof. Dr. Stan Harpole, Prof. Dr. Antonis Chatzinotas (funded by UFZ-IP, Helmholtz Association grant)
Head:
Scientific staff:
M. Sc. Peter Hofmann
Technician:
Student support of:
https://www.plantbiodiv.uni-jena.de/lehre MSc-Thesis Annalena Lenk, MSc-Thesis Till Deilmann, MSc-Thesis Nahid Rasouli Paeenroudposhti
Msc-Thesis Dorothea Leyrer (iNTERACT-project)
Former lab members:
Ridwan Jafaar (Erasmus student): Cross-boundary
nutrient and diversity effects of terrestrial plant pollen on freshwater
phytoplankton productivity
Daniel Lahr (Research associate): Implementation of iCyt workflow and AI training
Sumaira Saleem (Research associate) (2023): PlanktAI project, Phytoplankton identification via AI
Sophie Löbel -
Master student (2022/ 2023): Biological ice nuclei in air and rainwater
samples: studies on ice nucleating potential, macromolecular
composition and morphology (Co-supervision with Prof. Dr. Heike
Kalesse-Los, Dr. Susan Hartmann, Dr. Silvia Henning, Dr. Thomas Hornick)
Thomas Krautwig - Master student (2022/ 2023): Influence of macromolecular composition of pollen grains on their ice nucleation potential (Co-supervision with Prof. Dr. Heike Kalesse-Los, Dr. Susan Hartmann, Dr. Silvia Henning, Dr. Thomas Hornick)
Lea Reinke - Bachelor student (2022): Biotic interactions oft he cyanobacterium Microcystis aeruginosa and the green algae Oocystis marssonii
Nele Schildt - Bachelor student (2020): Investigation of species interaction between Chlamydomonas reinhardtii and Pseudomonas protegens with the help of imaging flow cytometry (Co-supervision with Prof. Dr. Severin Sasso, University of Leipzig)
Emily Scheil - Bachelor student (2020): Estimating the total pollen production in Carpinus betulus L. at the Leipziger Canopy Crane (Co-supervision with Prof. Dr. Christian Wirth, University of Leipzig)
Ella Schadt - Bachelor student (2020): Investigation of species interaction between Chlamydomonas reinhardtii and Pseudomonas protegens with the help of imaging flow cytometry (Co-supervision with Prof. Dr. Severin Sasso, University of Leipzig)
Johanna Knechtel - Bachelor student (2017): Quantification of allelopathic growth effects in mono and mixed cultures of microalgae (Co-supervision with Prof. Dr. Christian Wilhelm, University of Leipzig)
Photo credit: Stefan Bernhardt